Locus 1416

Sequence ID	X_DroMel_CAF1
Location	4,271,270 – 4,271,382
Length	112
Max. P	0.995908

overview

Window 6

Location	4,271,270 – 4,271,382
Length	112
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	95.92
Mean single sequence MFE	-22.70
Consensus MFE	-20.93
Energy contribution	-20.89
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.92
Structure conservation index	0.92
SVM decision value	2.63
SVM RNA-class probability	0.995908
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4271270 112 + 22224390
CCUCGACAAACAUUUGACCAUUGAAGCGCAUUUUUCGCUUGCGCGUCAUUUGUCAACUUGGCCGCUUCUUU--UUUUCAUUAUUUGCUUCUUUGCGAUUCUGCCACCCCUUGUU
....(((((....(((((...(((.(((((.........))))).)))...)))))..((((.........--..........((((......))))....))))....))))) ( -22.60)
>DroSec_CAF1 57896 112 + 1
CCUCGACAAACAUUUGACCAUUGAAGCGCAUUUUUCGCUUGCGCGUCAUUUGUCAACUUGGCCGCUUCUUU--UUUUCAUUAUUUGCUUCUUUGCGAUUCUGCCACCCCUUGUU
....(((((....(((((...(((.(((((.........))))).)))...)))))..((((.........--..........((((......))))....))))....))))) ( -22.60)
>DroSim_CAF1 52846 112 + 1
CCUCGACAAACAUUUGACCAUUGAAGCGCAUUUUUCGCUUGCGCGUCAUUUGUCAACUUGGCCGCUUCUUU--UUUUCAUUAUUUGCUUCUUUGCGAUUCUGCCACCCCUUGUU
....(((((....(((((...(((.(((((.........))))).)))...)))))..((((.........--..........((((......))))....))))....))))) ( -22.60)
>DroEre_CAF1 64961 111 + 1
CCUGGACAAACAUUUGACCAUUGAAGCGCAUUUUUCGCUUGCGCGUCAUUUGUCAACUUGGCCGCUUCUUU---UUUCAUUAUUUGCUUCCUUGCGAUUCUGCCGCCCCUUGUU
....(((((....(((((...(((.(((((.........))))).)))...)))))...(((.((......---.........((((......))))....)).)))..))))) ( -25.11)
>DroYak_CAF1 59414 114 + 1
CCUCGACAAACAUUUGACCAUUGAAGCGCAUUUUUCGCUUGCGCGUCAUUUGUCAACUUGGCCGCUUCUUUUUUUUUCAUUAUUUACUCCUUUGCGAUUUCGACGCCCCUUGUU
..((((....((.(((((...(((.(((((.........))))).)))...)))))..))..(((............................)))...))))........... ( -20.59)
>consensus
CCUCGACAAACAUUUGACCAUUGAAGCGCAUUUUUCGCUUGCGCGUCAUUUGUCAACUUGGCCGCUUCUUU__UUUUCAUUAUUUGCUUCUUUGCGAUUCUGCCACCCCUUGUU
....(((((....(((((...(((.(((((.........))))).)))...)))))..(((((((............................))).....))))....))))) (-20.93 = -20.89 +  -0.04)

alignment

secondary structure

dotplot

Window 7

Location	4,271,270 – 4,271,382
Length	112
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	95.92
Mean single sequence MFE	-25.33
Consensus MFE	-22.88
Energy contribution	-22.88
Covariance contribution	0.00
Combinations/Pair	1.08
Mean z-score	-1.77
Structure conservation index	0.90
SVM decision value	1.97
SVM RNA-class probability	0.984423
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4271270 112 - 22224390
AACAAGGGGUGGCAGAAUCGCAAAGAAGCAAAUAAUGAAAA--AAAGAAGCGGCCAAGUUGACAAAUGACGCGCAAGCGAAAAAUGCGCUUCAAUGGUCAAAUGUUUGUCGAGG
.(((((.(((.((......((......))......(....)--......)).)))...(((((...(((.(((((.........))))).)))...)))))...)))))..... ( -25.30)
>DroSec_CAF1 57896 112 - 1
AACAAGGGGUGGCAGAAUCGCAAAGAAGCAAAUAAUGAAAA--AAAGAAGCGGCCAAGUUGACAAAUGACGCGCAAGCGAAAAAUGCGCUUCAAUGGUCAAAUGUUUGUCGAGG
.(((((.(((.((......((......))......(....)--......)).)))...(((((...(((.(((((.........))))).)))...)))))...)))))..... ( -25.30)
>DroSim_CAF1 52846 112 - 1
AACAAGGGGUGGCAGAAUCGCAAAGAAGCAAAUAAUGAAAA--AAAGAAGCGGCCAAGUUGACAAAUGACGCGCAAGCGAAAAAUGCGCUUCAAUGGUCAAAUGUUUGUCGAGG
.(((((.(((.((......((......))......(....)--......)).)))...(((((...(((.(((((.........))))).)))...)))))...)))))..... ( -25.30)
>DroEre_CAF1 64961 111 - 1
AACAAGGGGCGGCAGAAUCGCAAGGAAGCAAAUAAUGAAA---AAAGAAGCGGCCAAGUUGACAAAUGACGCGCAAGCGAAAAAUGCGCUUCAAUGGUCAAAUGUUUGUCCAGG
......(((((((....((....))..((...........---......)).)))...(((((...(((.(((((.........))))).)))...)))))......))))... ( -28.43)
>DroYak_CAF1 59414 114 - 1
AACAAGGGGCGUCGAAAUCGCAAAGGAGUAAAUAAUGAAAAAAAAAGAAGCGGCCAAGUUGACAAAUGACGCGCAAGCGAAAAAUGCGCUUCAAUGGUCAAAUGUUUGUCGAGG
........(((.......))).............................((((....(((((...(((.(((((.........))))).)))...)))))......))))... ( -22.30)
>consensus
AACAAGGGGUGGCAGAAUCGCAAAGAAGCAAAUAAUGAAAA__AAAGAAGCGGCCAAGUUGACAAAUGACGCGCAAGCGAAAAAUGCGCUUCAAUGGUCAAAUGUUUGUCGAGG
.(((((.(((.((......((......))......(....)........)).)))...(((((...(((.(((((.........))))).)))...)))))...)))))..... (-22.88 = -22.88 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:54 2006